Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
98  structures 6255  species 0  interactions 10720  sequences 70  architectures

Family: ZT_dimer (PF16916)

Summary: Dimerisation domain of Zinc Transporter

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Dimerisation domain of Zinc Transporter Provide feedback

ZT_dimer is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 UniProtKB:O00244 exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side. The N-terminal part of the members is the Cation_efflux family, PF01545 [1].

Literature references

  1. Lu M, Fu D;, Science. 2007;317:1746-1748.: Structure of the zinc transporter YiiP. PUBMED:17717154 EPMC:17717154


This tab holds annotation information from the InterPro database.

InterPro entry IPR027470

The cation diffusion facilitator family (CDF) have members in both prokaryotes and eukaryotes, several of which have been shown to transport cobalt, cadmium and/or zinc. CDF transporters share a common two-modular architecture, consisting of a transmembrane domain (TMD) followed by a C-terminal domain (CTD) protruding into the cytoplasm [ PUBMED:9075641 ].

This entry represents the CDF C-terminal cytoplasmic domain. The cytoplasmic domain of Zinc transporter YiiP adopts a metallochaperone-like fold. The use of this common structural module to regulate metal coordination chemistry may enable a tunable transport activity in response to cytoplasmic metal fluctuations [ PUBMED:19749753 ]. It is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 ( SWISSPROT ) exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side [ PUBMED:17717154 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(363)
Full
(10720)
Representative proteomes UniProt
(42513)
RP15
(1597)
RP35
(5440)
RP55
(10238)
RP75
(16718)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(363)
Full
(10720)
Representative proteomes UniProt
(42513)
RP15
(1597)
RP35
(5440)
RP55
(10238)
RP75
(16718)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(363)
Full
(10720)
Representative proteomes UniProt
(42513)
RP15
(1597)
RP35
(5440)
RP55
(10238)
RP75
(16718)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_2qfi
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 363
Number in full: 10720
Average length of the domain: 77.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 22.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 26.7 26.7
Noise cut-off 26.6 26.6
Model length: 79
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ZT_dimer domain has been found. There are 98 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0EWT8 View 3D Structure Click here
A0A0R0F7R2 View 3D Structure Click here
A0A0R0GDG8 View 3D Structure Click here
A0A0R0IUI9 View 3D Structure Click here
A0A0R0L0L4 View 3D Structure Click here
A0A1D6HLS4 View 3D Structure Click here
A0A1D6K2U5 View 3D Structure Click here
A0A1D6MM34 View 3D Structure Click here
A0A1D6N7L6 View 3D Structure Click here
C0HGV8 View 3D Structure Click here
H2KZN1 View 3D Structure Click here
I1JDS7 View 3D Structure Click here
I1KTX5 View 3D Structure Click here
I1L2E9 View 3D Structure Click here
I1L2V9 View 3D Structure Click here
I1L7X1 View 3D Structure Click here
I1MJD0 View 3D Structure Click here
I1N523 View 3D Structure Click here
K7K8J1 View 3D Structure Click here
K7KF36 View 3D Structure Click here
K7M897 View 3D Structure Click here
O80632 View 3D Structure Click here
P69380 View 3D Structure Click here
P9WGF5 View 3D Structure Click here
Q0DHJ5 View 3D Structure Click here
Q0WU02 View 3D Structure Click here
Q10LJ2 View 3D Structure Click here
Q10PP8 View 3D Structure Click here
Q20864 View 3D Structure Click here
Q21304 View 3D Structure Click here
Q2FVK7 View 3D Structure Click here
Q3V5H6 View 3D Structure Click here
Q54N31 View 3D Structure Click here
Q57891 View 3D Structure Click here
Q5NA18 View 3D Structure Click here
Q5ZR77 View 3D Structure Click here
Q6Z7K5 View 3D Structure Click here
Q8L725 View 3D Structure Click here
Q9LDU0 View 3D Structure Click here
Q9M2P2 View 3D Structure Click here
Q9SAJ7 View 3D Structure Click here